A Semantic Web for bioinformatics: goals, tools, systems, applications

The quantity of biological information is increasing at an impressive rate. An integrated access to this huge amount of information requires complex search and retrieval software and automation of analysis processes. Automation of integration procedures mainly concerns how to link data, how to select and extract information and how to pipe retrieval and analysis steps. This automated approach to data analysis requires the adoption of new technologies and tools in the bioinformatics domain

Signaling in Posted Price Auctions

We study single-item single-unit Bayesian posted price auctions, where buyers arrive sequentially and their valuations for the item being sold depend on a random, unknown state of nature. The seller has complete knowledge of the actual state and can send signals to the buyers so as to disclose information about it. For instance, the state of nature may reflect the condition and/or some particular features of the item, which are known to the seller only. The problem faced by the seller is about how to partially disclose information about the state so as to maximize revenue. Unlike classical signaling problems, in this setting, the seller must also correlate the signals being sent to the buyers with some price proposals for them. This introduces additional challenges compared to standard settings. We consider two cases: the one where the seller can only send signals publicly visible to all buyers, and the case in which the seller can privately send a different signal to each buyer. As a first step, we prove that, in both settings, the problem of maximizing the seller's revenue does not admit an FPTAS unless P=NP, even for basic instances with a single buyer. As a result, in the rest of the paper, we focus on designing PTASs. In order to do so, we first introduce a unifying framework encompassing both public and private signaling, whose core result is a decomposition lemma that allows focusing on a finite set of possible buyers' posteriors. This forms the basis on which our PTASs are developed. In particular, in the public signaling setting, our PTAS employs some ad hoc techniques based on linear programming, while our PTAS for the private setting relies on the ellipsoid method to solve an exponentially-sized LP in polynomial time. In the latter case, we need a custom approximate separation oracle, which we implement with a dynamic programming approach

No short-term effects of geolocators on flight performance of an aerial insectivorous bird, the Barn Swallow (Hirundo rustica)

Miniaturized light-level geolocators are becoming increasingly popular devices for the study of avian migration. However, the effects of these devices on birds' flight behaviour, and hence fitness components, are poorly known. We investigated the effect of miniaturized geolocators on flight performance of the Barn Swallow (Hirundo rustica), which may be especially susceptible to geolocator deployment as it is a small (~20 g), aerially insectivorous, long-distance migratory species. We tested whether miniaturized geolocators (~3.5 % of body mass) affected short-term flight performance traits of breeding males by comparing flight manoeuvrability, velocity and acceleration of geolocator-equipped versus control (handled only) birds in flight tunnels. We used a robust experimental design wherein the within-individual change in flight performance was compared between geolocator-equipped birds (after allowing for a period of acclimation) and control birds (that were also tested twice). We found no statistically significant evidence that short-term flight performance traits were affected by geolocator deployment. Here we discuss the implications of our findings for the deployment of geolocators in studies of migratory behaviour of small birds

Expandable intramedullary nailing and platelet rich plasma to treat long bone non-unions

Background Roentgenographic and functional outcomes of expandable self locking intramedullary nailing and platelet rich plasma (PRP) gel in the treatment of long bone non-unions are reported. Materials and methods Twenty-two patients suffering from atrophic diaphyseal long bone non-unions were enrolled in the study. Patients were treated with removal of pre-existing ardware, decortication of non-union fragments, and fixation of pseudoarthrosis with expandable intramedullary nailing (FixionTM, Disc’O Tech, Tel Aviv, Israel). At surgery, PRP was placed in the pseudoarthrosis rim. Results The thirteen-month follow-up showed 91% (20/22 patients) of patients attaining bony union. The average time to union was 21.5 weeks. No infection, neurovascular complication, rotational malalignment, or limb shortening [4 mm were observed. The healing rate of non-unions was comparable to that observed in previous studies but with a lower complication frequency. Conclusions The combined use of self locking intramedullary nailing and PRP in the management of atrophic diaphyseal long bone non-unions seems to produce comparable results with less complications than previously reported. Further data are warranted to investigate the single contribution of PRP gel and Fixion nail

The compositional and mineralogical analysis of fired pigments in Nasca pottery from Cahuachi (Peru) by the combined use of the portable PIXE-alpha and portable XRD techniques

Abstract An analytical protocol based on the combined use of the portable PIXE-alpha (Particle Induced X-ray Emission) and XRD (X-ray Diffraction) non destructive techniques developed at the LANDIS laboratory (Laboratorio di Analisi Non Distruttive) of the INFN–CNR (Istituto Nazionale di Fisica Nucleare–Consiglio Nazionale delle Ricerche) in Catania (Italy), was applied for the characterisation of the surface paints of some archaeological fragments of Nasca pottery from the Ceremonial Centre of Cahuachi in Southern Peru. Measurements were carried out on the black, white, red, orange and grey pigments; quantitative information on the chemical composition as well as on the mineralogical phases present on the paints were obtained. Results allowed to make some considerations about the materials and the manufacturing technique used to realise such fired pigments. It should be noted that during firing the precursor minerals composing the pigments undergo a phase transformation and their identification presents some difficulties

On the use of virtual reality in software visualization: The case of the city metaphor

Background: Researchers have been exploring 3D representations for visualizing software. Among these representations, one of the most popular is the city metaphor, which represents a target object-oriented system as a virtual city. Recently, this metaphor has been also implemented in interactive software visualization tools that use virtual reality in an immersive 3D environment medium. Aims: We assessed the city metaphor displayed on a standard computer screen and in an immersive virtual reality with respect to the support provided in the comprehension of Java software systems. Method: We conducted a controlled experiment where we asked the participants to fulfill program comprehension tasks with the support of (i) an integrated development environment (Eclipse) with a plugin for gathering code metrics and identifying bad smells; and (ii) a visualization tool of the city metaphor displayed on a standard computer screen and in an immersive virtual reality. Results: The use of the city metaphor displayed on a standard computer screen and in an immersive virtual reality significantly improved the correctness of the solutions to program comprehension tasks with respect to Eclipse. Moreover, when carrying out these tasks, the participants using the city metaphor displayed in an immersive virtual reality were significantly faster than those visualizing with the city metaphor on a standard computer screen. Conclusions: Virtual reality is a viable means for software visualization

Indigenous yeast communities in the environment of ‘Rovello bianco’’ grape variety and their use in commercial white wine fermentation

The indigenous yeast communities associated with several vineyard habitats were analysed. Wild yeasts were isolated, differentiated at strain level and identified. A phylogenetic tree based on partial 26S rRNA genes was constructed. The strains were characterized and the indigenous Saccharomyces cerevisiae GR1 was then used to carry out a vinification process and compared with a commercial yeast. Wines obtained were subjected to chemical and sensory analysis. The comparison between the two products highlighted differences due to the fer- menting strains employed. The vineyard environment was found to strongly influence the composition of yeast communities, thus, confirming the theory of ‘terr- oir’ on the expression of wines. Moreover, vineyard inhabiting birds were in part responsible for the dis- semination of fermentative yeasts during their feedin